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RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans.

Jovanovic, M, Reiter, L, Clark, A, Weiss, M, Picotti, P, Rehrauer, H, Frei, A, Neukomm, LJ, Kaufman, E, Wollscheid, B , Simard, MJ, Miska, EA, Aebersold, R, Gerber, AP and Hengartner, MO (2012) RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans. Genome Res.

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Abstract

MicroRNAs (miRNAs) are small, noncoding RNAs that negatively regulate gene expression. As miRNAs are involved in a wide range of biological processes and diseases, much effort has been invested in identifying their mRNA targets. Here, we present a novel combinatorial approach, RIP-chip-SRM (RNA-binding protein immunopurification + microarray + targeted protein quantification via selected reaction monitoring), to identify de novo high-confidence miRNA targets in the nematode Caenorhabditis elegans. We used differential RIP-chip analysis of miRNA-induced silencing complexes from wild-type and miRNA mutant animals, followed by quantitative targeted proteomics via selected reaction monitoring to identify and validate mRNA targets of the C. elegans bantam homolog miR-58. Comparison of total mRNA and protein abundance changes in mir-58 mutant and wild-type animals indicated that the direct bantam/miR-58 targets identified here are mainly regulated at the level of protein abundance, not mRNA stability.

Item Type: Article
Authors :
NameEmailORCID
Jovanovic, M
Reiter, L
Clark, A
Weiss, M
Picotti, P
Rehrauer, H
Frei, A
Neukomm, LJ
Kaufman, E
Wollscheid, B
Simard, MJ
Miska, EA
Aebersold, R
Gerber, AP
Hengartner, MO
Date : 19 April 2012
Identification Number : 10.1101/gr.133330.111
Depositing User : Symplectic Elements
Date Deposited : 28 Mar 2017 14:42
Last Modified : 31 Oct 2017 14:33
URI: http://epubs.surrey.ac.uk/id/eprint/531404

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